Features and Functions of Bacteria Associated with Phytoplankton Blooms

REVIEWS

Master recyclers: features and functions of bacteria associated with phytoplankton blooms

Alison Buchan1, Gary R. LeCleir1, Christopher A. Gulvik2 and José M. González3 Abstract | Marine phytoplankton blooms are annual spring events that sustain active and diverse bloom-associated bacterial populations. Blooms vary considerably in terms of eukaryotic species composition and environmental conditions, but a limited number of heterotrophic bacterial lineages — primarily members of the Flavobacteriia, Alphaproteo- bacteria and Gammaproteobacteria — dominate these communities. In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling. On the basis of selected field and laboratory-based studies of flavobacteria and roseobacters, distinct metabolic strategies are emerging for these archetypal phytoplankton-associated taxa, which provide insights into the underlying mechanisms that dictate their behaviours during blooms.

Autotrophs Phytoplankton, such as diatoms and coccolithophores, in a patchy distribution of bacterial activity throughout 6 Organisms that convert are free-floating photosynthetic organisms that are the oceans . Copiotrophic bacteria, which swiftly capital- inorganic carbon, such as CO2, found in aquatic environments. These organisms capture ize on increased carbon and nutrient concentrations at into organic compounds. energy from sunlight and transform inorganic matter both the microscale and macroscale, complement their

Biological pump into organic matter (which is known as biomass). In the oligotrophic counterparts, which prefer dilute nutrient The export of phytosynthetically ocean, this organic matter is the foundation of a com- concentrations. Together, the heterotrophic bacteria, derived carbon via the sinking plex marine food web, which relies heavily on microbial which use these two distinct trophic strategies balance of particles from the illuminated transformation: approximately one-half of the carbon marine productivity. surface ocean to the deep that is fixed by marine autotrophs is directly processed by Microbially transformed carbon has several possible ocean. Approximately 0.1% of 1,2 (FIG. 1) the carbon that is fixed in the bacteria . The remaining carbon either enters the classic fates in the ocean ; for example, microbial respira- ocean is buried in marine marine food web or is transported as sinking particles tion converts carbon to an inorganic, gaseous state as sediments via this process. biological to the deep ocean for long-term storage via the CO2 that is released into the atmosphere. Phytoplankton- pump3 (FIG. 1). Localized and transient increases in the derived carbon can also enter the microbial loop, where it abundance of phytoplankton are referred to as blooms is first converted into microbial biomass and can either 1Department of Microbiology, and result in a boost in biogeochemical activities, includ- be transferred up the food web as bacteria succumb to University of Tennessee, ing the assimilation of CO2 and inorganic nutrients, predation by organisms at higher trophic levels (such Knoxville, Tennessee 4,5 37996-0845, USA. such as nitrogen and phosphorus . These processes are as zooplankton) or remain in the microbial domain 7 2School of Civil and partly balanced by a subsequent increase in the activity of via continual recycling . Alternatively, a fraction of the Environmental Engineering, heterotrophic bacteria, which transform phytoplankton- microbially transformed carbon is released into the dis- Georgia Institute of derived organic matter. As phytoplankton blooms are solved phase, some of which resists degradation and Technology, Atlanta, Georgia 30332, USA. often seasonal in nature and are thus transient events, contributes to the large pool of recalcitrant dissolved 3Department of Microbiology, the abundance and activity of heterotrophic bacteria organic carbon (DOC) that is stored in the ocean for University of La Laguna, varies accordingly. Indeed, secondary bacterial pro- thousands of years via the microbial carbon pump8. In ES-38200 La Laguna, Spain. duction typically correlates with the concentration addition, bacteria also regenerate nutrients that are Correspondence to A.B. of chlorophyll a, which is a proxy for phytoplankton associated with phytoplankton organic matter, particu- e-mail: [email protected] 2 7 doi:10.1038/nrmicro3326 abundance . This correlation between primary and larly nitrogen and phosphorus . Although it is not dis- Published online secondary production is evident on both small (that is, cussed in depth here, viral lysis of heterotrophic bacteria 19 August 2014 micromolar) and large (that is, basin) scales and results and phytoplankton is an important mechanism for the

686 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

CO2 Bacteria–phytoplankton interactions during bloom events are complex and change throughout the lifetime CO of the bloom. Bacteria can support the growth of phyto- 2 CO 2 plankton via the recycling of nutrients, but at the same time, they also compete with phytoplankton for essential nutrients. Both healthy and dead (or dying) phyto- 1 Phytoplankton Zooplankton plankton release organic compounds that are consumed 3 by heterotrophic bacteria, and the chemical nature and concentration of the released compounds varies with phytoplankton species and the physiological status of the phytoplankton10,11. Phytoplankton species show vari- 2 ation in their biochemical composition and the relative DOM POM cellular proportions of proteins, fatty acids, sugars and nucleic acids12–14. This variation in composition influ- DOC, DON and DOP POC, PON and POP ences both the stoichiometry, such as the C/N/P ratio, 4 and bioreactivity of phytoplankton-derived POM and Microbial loop DOM, which in turn influences the metabolic activity and proliferation of heterotrophic bacteria and dictates Heterotrophic their growth efficiencies as well as the fate of microbially P bacteria 6 P transformed organic matter . N P N Despite the variation in phytoplankton composition N and environmental conditions, a limited number of taxa Inorganic nutrients are consistently found to dominate bloom-associated Biological bacterial communities. The most frequent bacteria that pump 6 Microbial are identified by 16S ribosomal RNA gene-based sur- carbon pump 5 veys are members of the classes Flavobacteriia (hereafter 7 Viral shunt referred to as flavobacteria), Alphaproteobacteria, including members of the Rhodobacteraceae (such as roseobacters), and Gammaproteobacteria, such as members Long-term storage of the Alteromonadaceae15–17. The metabolic properties Figure 1 | Bacterial transformation of phytoplankton-derivedNature Reviews organic | Microbiology matter. The of these bacteria enable their ready response to transient marine carbon cycle includes a number of processes, several of which are mediated by nutrient pulses, which are a hallmark of phytoplankton microorganisms. Key processes of the marine carbon cycle include the conversion of blooms. Moreover, several laboratory studies have iden- inorganic carbon (such as CO2) to organic carbon by photosynthetic phytoplankton tified specific associations between phytoplankton and species (step 1); the release of both dissolved organic matter (DOM; which includes certain species of roseobacters and flavobacteria. As such, dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and dissolved organic these two bacterial groups have emerged as the main phosphorous (DOP)) and particulate organic matter (POM; which includes particulate models for the study of microorganism–phytoplankton organic carbon (POC), particulate organic nitrogen (PON) and particulate organic phosphorous (POP)) from phytoplankton (step 2); the consumption of phytoplankton interactions. This Review provides a brief overview of marine biomass by zooplankton grazers (step 3) and the mineralization (that is the release of CO2 via respiration during the catabolism of organic matter) and recycling of organic matter phytoplankton blooms and highlights recent advances by diverse heterotrophic bacteria, including, but not limited to, flavobacteria and in our understanding of the composition, dynamics and roseobacters (which is known as the microbial loop; step 4). A fraction of the physiologies of bloom-associated bacteria. Owing to the heterotrophic bacteria is consumed by zooplankton, and the carbon is further variation in the types of naturally occurring blooms, it transferred up the food web. Heterotrophic bacteria also contribute to the is difficult to depict a generalized bloom scenario that remineralization of organic nutrients, including DON and DOP, to inorganic forms, adequately encompasses the complexity of all of the which are then available for use by phytoplankton. The microbial carbon pump (step 5) observed systems. Instead, the objective here is to pro- refers to the transformation of organic carbon into recalcitrant DOC that resists further vide an overview of the most common bloom events and degradation and is sequestered in the ocean for thousands of years. The biological pump (step 6) refers to the export of phytoplankton-derived POM from the surface oceans to describe our understanding of microbial–phytoplankton deeper depths via sinking. Finally, the viral shunt (step 7) describes the contributions of interactions for flavobacteria and roseobacters, which viral-mediated cell lysis to the release of dissolved and particulate matter from both the are the two most well-described bacterial lineages phytoplankton and bacterial pools. (BOX 1). Data from both laboratory and field-based studies provide a framework for developing a mechanistic understanding of the factors that drive bacterial com- release of both dissolved organic matter (DOM) and par- munity composition and activity during phytoplankton Heterotrophic ticulate organic matter (POM) into the ocean. This viral blooms. Our ability to understand the roles that indi- A term used to describe an ‘shunt’ redirects carbon and nutrients away from higher vidual bacterial species have in both the formation of organism that uses organic trophic levels and towards the microbial realm9 (FIG. 1). blooms and their eventual collapse, will ultimately lead carbon compounds, such as Various biological and environmental factors determine to a better understanding of the forces that control dissolved organic matter and particulate organic matter, to how photosynthetically fixed carbon is processed by het- energy flow in the ocean as well as the cycling of com- satisfy its carbon requirement erotrophic bacteria in the ocean, and thereby determine pounds that influence climate change, including CO2 but that cannot fix carbon. its allocation among these reservoirs. and organosulphur compounds.

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 687

Box 1 | Defining the Roseobacter and Flavobacteria lineages although blooms are typically classified according to a dominant species that persists for the lifetime of the Although the use of the terms Roseobacter and Flavobacteria to describe bloom (BOX 2). Compared with natural blooms, experi- phylogenetically cohesive groups of marine bacteria is common in the microbial ecology mental phytoplankton blooms, which are generated literature, their use can be confusing as they do not conform to the Linnaean classification by the controlled use of defined nutrients, usually system. Members of the Roseobacter clade belong to the Rhodobacteraceae family in 27 the Alphaproteobacteria class of the Proteobacteria. The group name derives from the develop and collapse within 1 or 2 weeks . During both genus of the first two described strains (Roseobacter denitrificans and Roseobacter natural and experimental blooms, there is a high diver- litoralis), but the clade currently contains many more than the 50 described genera and sity of associated organisms that includes not only a thousands of uncharacterized species and strains. With few exceptions, all of the succession of phytoplankton but also a clear progression identified strains and 16S ribosomal RNA gene sequences that belong to this family are of protistan grazers, bacteria and viruses26,28–31. Bloom derived from marine or saline environments15. The polyphyletic nature of the decline may occur in response to ‘top-down’ forces (such Rhodobacteriaceae 16S rRNA gene makes phylogenetic reconstructions of the lineage as grazing and viral lysis), ‘bottom‑up’ forces (such as challenging74 and hinders the development of nucleic acid-based molecular tools that nutrient limitation) or a combination of both24,29,32,33. 125 are both specific and inclusive . It could be argued that the borders that define the The organic matter that is released by a declining bloom Roseobacter lineage are diffuse. Roseobacters were mostly ignored by microbiologists provides a wide range of nutritional resources, many of and ecologist until the early 1990s, when culture-independent approaches to assess microbial diversity were applied to marine systems and led to the recognition of this which can be exploited by the associated heterotrophic group as one of the most abundant bacterial groups in the oceans68. bacterial community. During bloom collapse, organic Flavobacteria is a term that is used to describe bacteria that belong to the molecules from dying phytoplankton frequently aggre- Flavobacteriia class in the Bacteroidetes phylum. Efforts have been made to decipher gate to form composites of detrital particles, which are the taxonomy of this phylum in recent decades, but the results have sometimes been readily colonized by heterotrophic bacteria34. Particle controversial126. This class currently contains a single order, the Flavobacteriales, and aggregation is mediated by large, sticky and acidic poly- four families (Flavobacteriaceae, Blattabacteriaceae, Cryomorphaceae and saccharides, which are collectively known as transpar- Schleiferiaceae), two of which (that is, Flavobacteriaceae and Cryomorphaceae) ent exopolymer particles (TEPs). TEPs can lead to the contain marine representatives. Most Blattabacteriaceae are obligate symbionts and formation of sinking detrital particles that transport the Schleiferiaceae family consists of a single genus (that is, Schleiferia). By contrast, phytoplankton material from surface waters to the Flavobacteriaceae is an extraordinarily diverse family that contains more than 100 35 genera, whereas the Cryomorphaceae family includes novel psychrotolerant genera deep ocean . (that is, genera that are tolerant to low temperatures)127. Both culture-dependent and Molecules that are produced by phytoplankton can -independent methods have determined the ubiquity of flavobacteria representatives also influence the climate on both local and global in diverse habitats, including the mammalian digestive tract, soil and aquatic scales. In addition to their involvement in aggregation environments113. Representative strains of flavobacteria have been readily isolated and transport, TEPs can be encapsulated and released from marine environments since at least the mid‑1950s128 and are found in various to the lower atmosphere via sea surface spray. Further- niches, but they are usually most abundant in coastal waters and in phytoplankton more, some phytoplankton produce large amounts blooms104. However, group members are frequently underrepresented in 16S rRNA of the organic sulphur compound dimethylsulphonio gene surveys as a result of technical difficulties — that is, standard primers for the 16S propionate (DMSP) during bloom events, which, as rRNA gene function poorly in flavobacteria104. Given the prevalence and culturability discussed below, can be converted to the gas dimethyl of both marine roseobacters and flavobacteria there has been increased interest in elucidating their metabolic potential and activities in the past 2 decades. Many of sulphide (DMS) via various biochemical pathways, some these investigations are facilitated by the availability of dozens of genome sequences of which are encoded by algae and some of which are 36 for isolated representatives or single cell amplified genomes (SAGs)77,110. encoded by members of the bacterial community . DMS emissions from surface seawaters are the major source of sulphur in the atmosphere37. Together with other marine Common features of phytoplankton blooms aerosols, both TEPs and DMS influence the regional and Most phytoplankton blooms develop in the spring global climate by functioning as cloud condensation nuclei months in response to higher intensity (or longer dura- and affecting solar backscattered radiation37,38. tion) of light exposure, combined with higher sea surface temperatures, reduced grazing pressure and higher Bacterial responses to phytoplankton blooms nutrient levels owing to seasonal mixing events18–20. Measurements of bulk community parameters have Depending on the biological, chemical and physical shown that phytoplankton blooms provide an environ- factors that control a given system, blooms can range ment that increases the rate of bacterial growth and from localized to massively scaled events (>100,000 km2 production30,39,40. The abundance of bacterial cells is Copiotrophic (FIG. 2) A term used to describe an ). Nitrogen, phosphorus, iron and silicate are generally positively correlated with the abundance of organism that thrives in, and is among the most common nutrients that influence both phytoplankton during the bloom (FIG. 2c). However, there well adapted to, high-nutrient the initiation and termination of a bloom, and the bal- is often an initial decoupling of bacterial and phyto conditions, unlike oligotrophic ance of these elements often drives the establishment plankton populations at the earliest stage of a bloom; organisms, which are adapted 21–24 to growth in low-nutrient of specific phytoplankton species . However, it is for example, an abrupt initial decrease in the abundance conditions. not yet clear if there is a single, globally dominant factor of bacterioplankton, followed by a subsequent increase, is that triggers the many spring phytoplankton blooms that frequently, but not always17, observed30 (FIG. 2c). The cause Microbial loop occur annually worldwide, and this remains an area of of the initial decline in bacterial abundance is not fully The microbial assimilation of active research and debate25. understood, but it might result from bacterial predation dissolved organic matter into 41 biomass and its transfer to Natural phytoplankton blooms typically last from by protists or from competition with phytoplankton 28 higher trophic levels as a result weeks to months and are characterized by a succession for nutrients . Irrespective of the cause, the bacterial of grazing by zooplankton. of several different phytoplankton species17,26 (FIG. 2), population rapidly recovers after the initial decrease

688 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

a and becomes abundant, as organic matter is released by the large phytoplankton population at the height of the bloom and during its decline. Indeed, the levels of bacteria remain high immediately following the collapse of a bloom, as bacteria continue to use the organic matter that is released from dying phytoplankton42. Changes in the abundance and types of phytoplank- A ton species, coupled with bacterial degradation of POM

Microbial carbon pump 50 km and DOM, alters both the concentration and composi- A process by which a major tion of the detrital pools at different times during the reservoir of dissolved organic b bloom, which, in turn, drives the composition and carbon is sequestered in the activity of the associated bacterial communities. In the ocean by a series of earliest stages of a bloom, phytoplankton release solu- heterotrophic microbial transformations of organic ble, labile, low molecular weight (LMW) molecules, matter, which renders it such as amino acids, organic acids, carbohydrates and increasingly resistant to sugar alcohols10,43,44, which might function as chemo biological degradation. B attractants for beneficial bacteria45, including bacteria

Dissolved organic matter that produce phytoplankton growth-promoting com- (DOM). The pool of organic pounds, such as vitamins. The release of small molecules matter that is operationally 50 km by living phytoplankton often increases in response to defined as that which passes nutrient-limiting conditions, which occur at the height through a filter with pores of of the bloom, and further stimulates heterotrophic bac- 0.22–0.45 µm in diameter. c 46,47 DOM can be further classified Bloom onset Bloom collapse terial activity . During the waning stages of the bloom, on the basis of bioavailability. phytoplankton release higher molecular weight macromolecules (HMW), including polysaccharides, proteins, Particulate organic matter nucleic acids and lipids, as well as particulate material, (POM). The pool of organic 6,11,48 matter that is operationally primarily as result of cell lysis , although several 35 defined as that which is HMW compounds are also released from viable cells , retained on a filter with pores perhaps to sustain mutualistic interactions with the of 0.22–0.45 µm in diameter. bacterial community. Relative abundance Cloud condensation nuclei Aerosols (that is, liquid droplets Bacterial conversion of organic matter. Bloom-associated or solid particles) suspended in heterotrophic bacteria are fuelled by the assimilation the air that lead to the Time (weeks) and remineralization of phytoplankton organic matter. condensation of water vapour Owing to the heterogeneous chemical nature of this to form clouds. Bacteria Nanoﬂagellates Picophytoplankton organic matter, the processes involved are complex Diatoms Dinoﬂagellates 49,50 Solar backscattered and are not yet fully understood . An initial step radiation in the transformation of the bioavailable particulate Figure 2 | A representativeNature bloom Reviews in the southern | Microbiology Solar radiation from the sun Pacific Ocean. Spring phytoplankton blooms are a fraction of organic matter is its conversion to the dis- that is reflected back towards natural part of the seasonal productivity cycle of many solved phase (that is, DOM), which enables transport space by the atmosphere, marine systems. These blooms are transient events that clouds and the surface of the across the bacterial cell wall. This conversion is influ- Earth. typically last for several weeks and are large enough to enced by many factors, but the main requirement is the be visible from space. a | A satellite image of the eastern availability and action of extracellular and cell surface- Bacterioplankton coast of New Zealand before a bloom on 11 October associated enzymes6. Indeed, shifts in substrate-uptake Free-living, planktonic bacteria 2009 is shown. b | The satellite image shows the same 31 and archaea that reside in an capabilities , increases in extracellular and cell surface- region during a diatom-dominated bloom on 29 October 17,30 aquatic system. 2009. Such blooms are annual occurrences in this region associated hydrolytic enzyme activities and changes and the phytoplankton composition of these blooms in the hydrophilic and hydrophobic properties of the 51 Linnaean classification have been characterized26. c | The graph shows a typical bacterial cell surface have been documented in bloom- system succession of phytoplankton groups during the course associated bacteria. Furthermore, senescent phyto- The taxonomic nomenclature that was developed by Carl of a spring phytoplankton bloom in this region of the plankton cells and aggregates are rapidly colonized by Linnaeus, in which distinct ocean, which often lasts for many weeks (data taken bacteria that have a full range of hydrolytic enzymes hierarchical groups, such as from REF. 26). Changes in the relative abundance of for efficient particle solubilization, and high extracel- phylum, class, order, family, heterotrophic bacteria and nanoflagellate grazers are lular enzyme activities have been reported for bacteria genus and species are defined. also indicated to show the increase in bacterial that are attached to senescent diatom cells34. After this abundance in response to increases in phytoplankton, initial conversion of POM, DOM is rapidly assimilated Remineralization in addition to the increase in grazers in response to The transformation of organic increases in their prey populations (such as bacteria and into microbial biomass and a fraction of the carbon is matter to an inorganic form. phytoplankton). The satellite images were captured by respired as CO2. This term is most often used to It should be noted that not all phytoplankton- describe the conversion of the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA Aqua satellite during the 2009 austral derived organic matter is susceptible to microbial organic carbon to CO2, which is a central component of the spring and were generated by R. Simmon and J. Allen, attack: a substantial fraction (~30%) of the DOM that is carbon cycle. Ocean Colour Team, NASA, USA. released from phytoplankton is recalcitrant to microbial

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 689

Box 2 | The dominant marine phytoplankton that are associated with blooms The biogeochemical impact of phytoplankton blooms is strongly influenced by the dominant bloom-forming species. Some of the major groups of blooming, unicellular marine phytoplankton are the diatoms, coccolithophores and Phaeocystis spp. (see the figure). Diatoms Diatom-dominated blooms are common in coastal oceans and upwelling zones, in which nutrient levels are high in the euphotic zone129. Indeed, diatoms are often the major photoautotroph of spring phytoplankton blooms in temperate coastal oceans and freshwater environments130 (see the figure, part a). Diatoms are responsible for nearly one-quarter of the global primary production131 and 40% of marine primary production, which involves the synthesis of organic

compounds from CO2 (REF. 132). Thus, these blooms affect benthic zone and pelagic zone food webs and are crucial for sustaining fish populations in temperate seas129. Compared with other phytoplankton, diatoms tend to be highly competitive under the environmental conditions that are characteristic of spring, such as high nutrient concentrations, cooler temperatures and substantial variations in light exposure. Silicate is required for the synthesis of their outer cell wall (known as a frustule)133, which is exclusive to diatoms, and structural variations between species yield a range of unique skeletons. Following diatom cell death and decomposition, the frustules sink and accumulate in marine sediments, producing diatomite, which is an important component of fossils and also has a commercial application as diatomaceous earth130. It has been suggested that silicate depletion is a primary factor that determines the decline of diatom blooms24. Part a of the figure shows the diatom Thalassiosira pseudonana134. Coccolithophores Coccolithophorids, specifically Emiliania huxleyi, are marine microalgae that form extensive, seasonal blooms and that have cell densities typically in the range of 10,000 cells per ml of water21. Similarly to diatoms, coccolithophores also have a

distinct outer layer, known as the coccolith, which is composed of calcium carbonate (CaCO3) and is also an important 135 component of the fossil record . The sinking of CaCO3-rich coccolithophorids and their burial in marine sediments leads to

loss of CO2 from the upper water layer; thus, they represent an important mechanism for CO2 sequestration. This export of

organic matter and CaCO3 from surface waters is a vital component of the oceanic biological pump, which transports carbon 136 137 to the depths of the ocean (FIG. 1). Coccolithophore blooms are major sinks of CO2 in the global oceans , and these organisms also produce the organic sulphur compound dimethylsulphoniopropionate (DMSP), which is both an important source of sulphur to the atmosphere and an important source of carbon and reduced sulphur for some heterotrophic marine bacteria. Coccolithophores are uncommon in freshwater systems owing to low calcium concentrations138. The main coccolithophore in the oceans is E. huxleyi139,140 (see the figure, part b). This species can form massive blooms, particularly in phosphorous‑limited conditions22. Such blooms are often visible from space owing to the reflective nature of coccoliths137, and several studies have suggested that E. huxleyi viruses have a role in bloom termination141. Phaeocystis spp. Phaeocystis spp. is another common bloom-forming phytoplankton that produces DMSP23. A characteristic property of this genus is its ability to grow as a floating colony that comprises several hundred cells embedded in a polysaccharide gel Euphotic zone 142 143 The layer of the water column matrix , which can compromise water quality . Some of the largest Phaeocystis spp. blooms occur in polar and subpolar 144 that receives sufficient light to regions , where they might avoid grazing by zooplankton via the production of transparent exopolymer particles (TEPs) 145 support photosynthesis. This and/or growth in either the colonial form or as single cells . It is estimated that members of this genus are responsible for zone is usually the upper 200 ~10% of the annual global primary productivity23. Part c of the figure shows the prymnesiophyte Phaeocystis globosa146. metres, but the lower Part a of the figure is reproduced, with permission, from REF. 134, © 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. boundary varies as the Part b of the figure is reproduced, with permission, from REF. 140 ©2012. American Geophysical Union. All Rights concentration of living and Reserved. Part c of the figure reprinted from J. Sea Res., 76, Rousseau, V. et al., Characterization of Phaeocystis globosa non-living particles change the (Prymnesiophyceae), the blooming species in the Southern North Sea, 105–113, © (2013), with permission from Elsevier. turbidity of the water. a b c Benthic zone The region of the water column that extends from immediately above the sediment surface to immediately below the sediment surface. Sinking material, such as marine snow, accumulates in this zone. 1 μm 5 μm 1 μm Pelagic zone The upper region of the water column that is distant from Nature Reviews | Microbiology land and from the seafloor. degradation8. Furthermore, microbial transformation of centuries to millennia)53. Thus, some metabolically Water turbidity and light intensity do not shift the organic matter results in a range of metabolic products transformed products of phytoplankton organic mat- demarcation of the pelagic that are remarkably different from the original material. ter can be resistant to further bacterial transformation zone. For example, the preferential use of the nitrogen compo- and can thus contribute to both short-term and long-term nent of both DOM and POM by natural heterotrophic carbon storage in the oceans8,54. Diatomaceous earth bacterial populations is common52, and this leads to an The remaining particulate matter from dead and decayed increased C/N ratio in increasingly processed organic Bacterioplankton community structures. Changes in the diatoms, which are heavily matter, which is characteristic of recalcitrant material abundance and species composition of phytoplankton enriched in silica frustules. (that is, material that resists microbial degradation for during blooms leads to corresponding changes in the

690 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

bacterial community17,30,55 (FIG. 3a). The temporal scale success of individual taxa. Owing to the substantial of these shifts is often determined by factors that initiate physiological and genomic information that is available the bloom, such as the type and concentration of nutri- for roseobacter and flavobacteria strains, the study of ents, as well as temperature. As naturally occurring phy- these bacteria can complement and enable the interpreta- toplankton blooms are generally more gradual in their tion of functional community analysis data17. As the same development and demise than experimental blooms, the level of detail is unavailable for the Gammaproteobacteria, shifts in bacterial community structure typically occur this class is not discussed. over a longer timescale. As different phytoplankton spe- Analysis of bacterial populations using higher phylo- cies release different forms of organic matter and as het- genetic resolution (that is, at the species and subspecies erotrophic bacteria differ in their capacity to consume levels) reveals that closely related roseobacter and flavo- and remineralize various substrates56–58, it is predicted bacteria phylotypes frequently show considerably differ- that bacterial community structure is strongly influ- ent responses during bloom progression. For example, enced by the composition of the phytoplankton species, during a North Sea diatom bloom succession, three dif- and this is supported by studies of several blooms55,59,60. ferent phylotypes of flavobacteria (that is, Ulvibacter-, By contrast, a recent study in the South Pacific ocean Polaribacter- and Formosa-related) and two roseobacter found that two distinct bloom events, in which differ- phylotypes (that is, DC5‑80‑3 and NAC11‑7) showed ent proportions of diatoms and cyanobacteria were contrasting abundance patterns throughout the bloom17 observed, shared highly similar bacterial communities61. (FIG. 3b). This suggests that there is a high degree of niche Phylogenetic analyses of bacterioplankton have been specialization among these closely related taxa. Although carried out on both experimental and natural blooms, we currently know little about the role of individual bac- and the higher-order taxonomic classifications of the terial phylotypes during these dynamic events, genome most abundant bloom bacteria are now well defined. and culture-based studies of representative roseobacter However, such studies often differ with respect to bloom and flavobacteria strains are providing valuable insights location, duration and intensity of sampling, phyto- into the nature of potential interactions. plankton species succession, geochemistry and temperature, which prevents quantitative generalizations Physiologies of bloom-associated bacteria of bacterial composition and responses. Nevertheless, Unlike many of the other major marine bacterial line- a few bacterial lineages within the Proteobacteria and ages, such as the SAR86 and SAR116 clades, which are Bacteroidetes are typically abundant in blooms, irre- either difficult to culture or have not yet been brought spective of the dominant phytoplankton species55,62,63. into culture, there are cultivated representatives available More detailed bacterial responses to bloom conditions, for flavobacteria and roseobacter68. Indeed, cultivated which involve comprehensive time-series analyses of representatives from these two groups are frequently both environmental and biological factors before, dur- isolated from blooms and in vitro enrichment cultures ing and after a bloom have recently been reported17,61. of different phytoplankton60,69,70, and they have even been As discussed below, these studies have shown that the found to directly attach to phytoplankton cells during relative abundance of the different bacterial phyla and a bloom71. The activities of these bacteria can be either subphyla vary during the time course of a single bloom, supportive of or inhibitory to phytoplankton growth, as well as between different blooms. By contrast, the few and this seems to vary according to the age of the bloom studies that have examined archaeal abundance and and local environmental conditions72. These findings diversity show that the abundance of these organisms suggest that there is an intimate and dynamic rela- decreases during blooms, which suggests that they are tionship between specific bacterial strains and their outcompeted by bacteria and phytoplankton for nutri- phytoplankton hosts, which probably has ancient ori- ent resources under bloom conditions64. Although phage gins, given that bacteria and eukaryotic phytoplankton abundance can be estimated from microscopy, relatively have coexisted in the oceans for more than 200 million little is known about the specific roles that phages have years73,74. In fact, the nature of these bacterial–phyto- in controlling bacterial composition and abundance65, plankton interactions ranges from mutualistic to para- but this is an emerging area of interest. sitic. Some bacteria provide their hosts with essential Roseobacters, flavobacteria and members of the vitamins and nutrients and provide protection against Gammaproteobacteria are typically the most dominant toxic metabolic by‑products, whereas others compete bacteria in blooms, and the abundance of these groups with their hosts for nutrients or produce algicidal com- (which is determined by 16S rRNA gene surveys) often pounds. Several examples of the interactions between correlates with the succession patterns of phytoplank- diatoms and their associated bacteria are available in a ton populations30,55,62. Functional community analysis recent and comprehensive review75. In the following sec- approaches have recently been used, including metagen- tions, we mainly discuss the physiological processes that omic, metatranscriptomic and metaproteomic studies, are involved in the bacterial transformation of phyto- and these have provided a more holistic view of bacte- plankton-derived organic matter, particularly those that Phylotypes rial activities17,66,67. Despite their value, these studies often occur in the context of a bloom. Sequences or groups of consider only higher-order taxonomic groups, and as sequences that share a certain level of homology, which such, much of the biodiversity is masked. Furthermore, Roseobacters. Given both the abundance of roseobac- enables evolutionary these types of studies reveal little about the potential ters in marine systems and the availability of cultured relatedness to be inferred. physiological or mechanistic factors that lead to the representatives, this group has been the focus of many

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 691

a 14 4.0 ecological, genomic and physiological studies. In this section, we discuss the features of this group that are 3.5 12 predicted to be important and relevant to phytoplankton

Bacterial abundance blooms, but it should be noted that not all observations 3.0

) have been confirmed within the context of phytoplankton 3 10 blooms. 2.5 Members of the Roseobacter lineage are involved in 8 key biogeochemical processes, including carbon, nitro- (mg per m a 2.0 gen, phosphorus and sulphur transformations, several of which are expected to be important for interactions

6 ×

10 15,76 1.5 with phytoplankton . Roseobacter isolates have larger

6 77 pe r ml genomes (~4.5 Mb) and higher gene content than Chlorophyll Chlorophyll 4 1.0 other abundant marine lineages that are geographi- cally limited to the nutrient-poor open ocean (such as 78,79 2 0.5 Prochlorococcus spp. and Pelagibacter spp.) , which might be key to the ecological success of this group.

0 0 Although an analysis of the collective genetic comple- 1 48 55 62 69 76 83 90 ment of roseobacters shows that the group encodes sev- Day eral biogeochemically relevant pathways, only a subset b of these pathways are present in any single genome77. 3.9 9.4 6.5 29.8 9.2 54.5 10.5 33.0 7.7 41.9 20.7 41.9 6.3 29.2 6.3 18.3 Roseobacter Indeed, it is becoming clear that a specific set of genes Other or metabolic capabilities is not representative of the Roseobacter AS-21 lineage as a whole. Furthermore, genome analysis of Roseobacter OCT uncultivated phylotypes suggests that at least some mem- Roseobacter NAC11-7 bers have relatively small genomes (such as phylotype 80 Roseobacter DC5-80-3 HTCC2255, which has a 2.2 Mb genome ) and differ in terms of functional attributes, compared with a collection of cultivated strains81. These most recent find- Flavobacteria ings suggest that the ecological r‑strategist model, which Other is often used to describe roseobacters, may not be as NS9 broadly applicable to the group as previously suggested Winogradskyella and highlight that niche adaptation (including whether Ulvibacter a bacterium is typically phytoplankton-associated or Tenacibaculum free-living) drives the variation in both genome size and Suﬄavibacter content among lineage members74. Polaribacter The idea that Roseobacter lineages form intimate

Roseobacter and ﬂavobacteria reads (%) Roseobacter and ﬂavobacteria reads NS5 marine group relationships with both macroalgal and microalgal cells NS4 marine group predates the implementation of culture-independent 82 NS3a marine group studies of environmental bacteria and is mostly sug- Formosa gestive of mutualistic, and potentially obligate, interac- 60,83–85 Flaviramulus tions . However, recent studies suggest that some Cryomorphaceae specific interactions have tipped the balance from mutu- 1 48 55 62 69 76 83 90 alistic to pathogenic, owing to the production of algicidal 72,86 Day compounds , which may be important during the terminal stages of the bloom, when nutrient resources Figure 3 | Changes in the abundance of roseobacter andNature flavobacteria Reviews | Microbiology phylotypes during a diatom-dominated bloom. A high-resolution analysis of the bacterial become limiting. As a result, phytoplankton are pos- community during a natural spring diatom-dominated phytoplankton bloom in the sibly more susceptible to such compounds. Indeed, North Sea shows the succession of specific roseobacter and flavobacteria phylotypes. a recent study suggests that a mutualistic relationship a | Chlorophyll a measurements are a proxy for phytoplankton abundance during the can easily become pathogenic, depending on specific course of the 90 day survey. Despite the coarse temporal resolution, it is evident that the environmental or biological cues, including the onset increase in bacterial abundance coincides with the decline in phytoplankton (following of senescence in a phytoplankton culture72. Symbioses an initial surge), which is probably due to the increased availability of phytoplankton between roseobacters and specific phytoplankton are organic matter fuelling bacterial growth. b | Compared with all other bacteria, the probably facilitated by several common characteristics relative abundance of roseobacters and flavobacteria increased during the bloom. The (FIG. 4), including chemotaxis towards compounds that values above each stacked column represent the percent abundance of each group are released by phytoplankton (for example, DMSP and member relative to total bacteria, as determined by 16S ribosomal RNA gene sequence 45 analysis. The relative abundances of roseobacters and flavobacteria, as well as specific amino acids) , as well as the uptake and use of various phylotypes (as indicated in the key), are dynamic throughout the bloom. These complex phytoplankton-derived compounds, such as DOM, dynamics are probably the result of tight coupling between these heterotrophic bacteria which are sources of carbon, sulphur, nitrogen and/or and changing local environmental conditions, which are expected to be primarily phosphorus (for example, DMSP, urea, polyamines, tau- mediated by alterations in the availability of phytoplankton-derived organic matter and rine, glycine betaine, methylated amines, phosphoesters possibly inorganic nutrient levels. Data taken from REF. 17. and phosphonates)77,87–89. Genomic approaches have

692 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

identified transporters, including those of the TRAP (tripartite ATP-independent periplasmic), MFS (major facilitator superfamily) and ABC (ATP-binding cassette) families, which are probably specific for these substrates DMS and are abundant in the genomes of roseobacters77,87. The production of secondary metabolites is often the basis of chemical signalling, defence and host– microorganism interactions90, and many roseobacters produce a range of bioactive compounds, including signalling molecules and antimicrobial compounds (FIG. 4). Phytoplankton The production of these two types of molecules is often linked91–93 and may facilitate intimate interactions with algal hosts. Several roseobacters produce quorum sens- DMSP ing molecules, particularly N‑acyl-homoserine lactones DOM (AHLs). So far, the AHLs that have been characterized Receptors from roseobacter isolates have some of the longest rec- 94 ognized acyl side chains (that is, C8–C18) . In addition, Flagellar DMS + acrylate MeSH novel quorum sensing compounds have been identi- motor fied, including p‑coumaroyl-homoserine lactone, the Chemotaxis proteins Adhesive production of which requires an exogenous supply + H structure of the aromatic compound p‑coumaric acid95, which ABC-type might be released by decaying phytoplankton72. Anti- transporters DMT transporter microbial molecules, including tropodithietic acid and ADP ATP indigoidine, have been identified, and studies that are ATP Secondary hv synthase aimed at linking the production of these secondary transporter H+ POM 93,96 H+/Na+ metabolites to bacterial fitness are underway . The Bacteriochlorophyll a production of growth-promoting compounds, includ- Antimicrobials ing auxins and vitamins, by roseobacters has been proposed to facilitate mutualism with phytoplank- 70,72,77,87 AHLs ton , and transport proteins that belong to the Vitamins drug–metabolite (DMT) superfamily are anticipated to be involved in the export of such compounds87. Surface-associated structures, including those that resemble holdfasts, are also common among character- Figure 4 | Physiological features of roseobacters that facilitate associations with ized roseobacter isolates, are important in attachment phytoplankton. Roseobacters have many metabolic featuresNature that Reviews probably | Microbiology facilitate 97 interactions with phytoplankton and phytodetrital material. The organic sulphur to organic particles and may facilitate attachment to compound dimethylsulphoniopropionate (DMSP) is produced by phytoplankton and the surfaces of living phytoplankton cells. Indeed, the transformed via one of two pathways: cleavage to form dimethyl sulphide (DMS) roseobacter isolate Ruegeria sp. TM1040 was found to and acrylate or demethylation to form methanethiol (MeSH). DMS is volatile and form biofilms on the Pfiesteria-like dinoflagellate in fluxes to the atmosphere, where it contributes to cloud formation, whereas the acrylate culture98. Finally, aerobic anoxygenic phototrophy (AAP) by‑product can be used as a carbon source by the bacteria. MeSH is also a valuable is evident in many isolated strains as well as envi- carbon substrate, from which reduced sulphur is derived. Indeed, roseobacters use a ronmental genomes. This type of photoheterotrophic wide range of low molecular weight, phytoplankton-derived compounds as sources of strategy requires the capture of energy from sunlight carbon, nitrogen and phosphorus (depicted as dissolved organic matter (DOM)). by photopigments (such as bacteriochlorophyll a and Chemotaxis towards several of these phytoplankton-derived compounds has been carotenoids) and the translocation of protons across the demonstrated and roseobacters encode several transport systems that are predicted to mediate the uptake of small molecules, including ATP-dependent transporters (such as membrane, which produces a membrane electrochemi- ATP-binding cassette (ABC) transporters) and secondary transporters that may use cal gradient that can be used for the production of ATP electrochemical gradients to mediate membrane translocation, such as TRAP (tripartite (via ATP synthases), active transport (by secondary ATP-independent periplasmic) and drug–metabolite (DMT) type systems. TRAP transport via TRAP and DMT-type transporters) and transporters are thought to import carboxylic acids, whereas DMT transporters are motility70,82 (FIG. 4). As discussed below, light-driven ion thought to export secondary metabolites, including phytoplankton growth-promoting pumps are also common in flavobacteria, but the con- compounds (such as auxins and vitamins) and antimicrobial compounds that may tribution of these photoproteins to bacterial activities provide roseobacters with a competitive advantage when colonizing the surfaces of in the ocean is not yet understood. phytoplankton. Quorum sensing signalling molecules, typically N‑acyl homoserine An excellent example of the tight coupling between lactones (AHLs), are produced by many roseobacter strains and have been shown to roseobacters and phytoplankton comes from the study regulate the production of antimicrobial compounds in a cell density-dependent manner. In addition to the oxidation of organic matter, many roseobacter genomes of a single algal osmolyte, DMSP. DMSP accounts for up encode bacteriochlorophyll a‑based light-driven proton pumps that contribute to to 10% of the carbon that is fixed by marine phytoplank- membrane electrochemical gradients, which can be used to generate ATP via ATP ton in the sunlit layers of the ocean99, and it is produced synthases, facilitate transport or drive flagellar motors. Adhesive structures for by several species of phytoplankton, by macroalgae and attachment to surfaces are also commonly observed in roseobacter isolates. POM, by some aquatic vascular plants36. Concentrations of particulate organic matter. DMSP inside dinoflagellates and prymnesiophytes, such

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 693

as Emiliania huxleyi and Phaeocystis spp., can reach the dominant phytoplankton species, geochemical condi- molar range99. During the demise of phytoplankton cells, tions and geographic location17,64,114, have been carried particulate-bound DMSP is transferred to the dissolved out so far, common functional patterns are evident, phase via grazing, autolysis and viral lysis100. The dis- particularly for flavobacteria. Metaproteomic profiling solved DMSP is readily available for bacterial degrada- of both North Sea and Southern Ocean phytoplankton tion, and it functions as a valuable carbon and sulphur blooms have shown that TonB-dependent transporter source for those cells that have the proteins and enzymes (TBDT) systems that are representative of those found that are needed for its uptake and degradation. In fact, in flavobacterial isolates are abundant during the peak DMSP-degrading marine bacteria can satisfy nearly all of blooms17,64. Typically, TBDT systems contain outer of their sulphur demand by DMSP consumption alone101. membrane substrate-binding proteins and cell sur- Although sulphur concentrations are not limiting in sea- face-associated degradative enzymes (such as glycosyl water, the reduced form that is present in DMSP is more hydrolases), which collectively facilitate the use of HMW energetically useful to marine bacteria than the oxidized macromolecules that are present in DOM115 (FIG. 5). This form that is found in seawater sulphate. Many culti- is in contrast to LMW transport systems, such as the vated Roseobacter lineages are capable of transforming ABC-type and secondary transporters (that are spe- DMSP, either by cleavage (to form DMS and acrylate) cific for free amino acids, sugars and monocarboxylic Ecological r‑strategist model or by demethylation (to form methanethiol (MeSH))36. or dicarboxylic acids), which are frequently mapped to Model organisms with 17,114 relatively large genomes that DMS is volatile and readily escapes into the atmosphere, roseobacters during blooms . In fact, the number of encode diverse metabolic where it is proposed to contribute to the formation of transporters that are encoded in marine flavobacteria capabilities, which enable them cloud condensation nuclei and to the backscatter of solar genomes is remarkably low compared with most other to rapidly respond to increases radiation37. MeSH is more likely to remain in the sur- copiotrophic marine bacteria, including roseobac- in carbon and nutrients. face ocean, where it is readily used by marine bacteria ters108,113,116. Carbohydrate-active enzymes that degrade (FIG. 4) Phytodetrital material . Thus, the DMSP cleavage pathway has important algal polysaccharides (such as laminarinases, which Non-living organic matter that implications for global climate regulation, whereas the degrade laminarin, and β‑D‑fucosidases, which degrade is derived from phytoplankton. DMSP demethylation pathway is important for supply- fucose) have been found to coincide with the peak abun- ing carbon and sulphur to marine food webs. Roseo- dances of flavobacteria17,64. Finally, rhodopsins, which Auxins A class of hormones that bacters can possess either the demethylation pathway support photoheterotrophic growth via the light-driven 77 stimulate growth and regulate or the cleavage pathway, and some strains have both . membrane translocation of protons and sodium ions, the behaviour of phototrophs. Indeed, the roseobacter strain Ruegeria pomeroyi, which may contribute to the formation of electrochemical gra- has a DMSP demethylase gene (dmdA), as well as three dients and are found in both flavobacterial isolates and Holdfasts DMSP lyase orthologues (dddP, ddpQ and dddW)77,102, in the SAGs of marine flavobacteria107,110 (FIG. 5). In addi- Adhesive structures that facilitate the attachment of a is proving to be a valuable strain for studies aimed at tion, proteomic data indicate that rhodopsin is produced 64 cell to a surface. understanding the regulation of DMSP transformation during phytoplankton blooms . Although it has been by marine bacteria. proposed that flavobacteria have a bimodal lifestyle, in Aerobic anoxygenic which they could simultaneously derive energy from the phototrophy A photoheterotrophic strategy Flavobacteria. Like roseobacters, flavobacteria are oxidation of organic compounds and light-driven ion- 107 in which bacteriochlorophyll a found outside phytoplankton blooms. Global ocean pumping rhodopsins , the extent to which this addi- reaction centres are excited by surveys suggest that flavobacteria are most abundant in tional energy source supports these populations is not the absorption of light and upwelling, temperate to polar oceans and coastal regions, entirely clear in the context of phytoplankton blooms pass electrons through a series and that open ocean bacterial communities typically that are rich in organic matter. In addition to the light- of carrier proteins that pump protons out of the cell, which contain 10–20% Bacteroidetes, most of which are flavo- driven membrane translocation of ions, a flavobacterium 103,104 contributes to the bacteria . In the context of phytoplankton blooms, rhodopsin that pumps chloride ions was recently char- electrochemical gradient of the flavobacterial abundance is typically highest during the acterized and is probably involved in the maintenance cell. decay phase30,55,105, and it has been proposed that a pri- of osmotic balance117.

Photoheterotrophic mary role for members of this group is the conversion The association between phytoplankton and flavo- 17 A term used to describe a of HMW compounds into LMW compounds . In fact, bacteria is likely to be more complex than the ability of heterotroph that uses light analysis of the gene content of sequenced isolates106–109, flavobacteria to transform HMW compounds. A key (that is, photons) to fuel as well as the genomes of uncultured environmental rep- aspect that is required for the efficient degradation of energy-requiring metabolic resentatives (that is, single amplified genomes (SAGs) particulate matter is the adhesion of bacteria to the sub- processes. derived from cells isolated by flow cytometry, but not strate. The production of polymer-degrading enzymes 110 111 Fosmid libraries cultivated) and fosmid libraries predicts that at least that target host cellular components, such as the cell Libraries of cloning vectors some flavobacteria are better adapted to using complex wall, is a common feature of Bacteroidetes116. Genes that derived from the bacterial substrates than simple, monomeric compounds112. The encode products that are predicted to be exported out of F plasmid that stably maintain large fragments of DNA and ability of flavobacteria to use a broad range of biopoly- the cell and that mediate the breakdown of eukaryotic are often used for sequencing mers, particularly polysaccharides and proteins, as pri- cells, such as proteases, have been found in flavobacteria or phenotypic screening. mary carbon and energy sources can explain the varied genomes108. In addition, new taxa of flavobacteria that interactions that these bacteria seem to have not only show microalgicidal activity have been described118,119, Rhodopsins with eukaryotic phytoplankton but also with marine and several flavobacterial isolates have been found to Transmembrane proteins that 113 120 function as light-driven ion vertebrates and mammals . cause disease in macroalgae, particularly red algae . pumps; they are present in all Although only a few metatranscriptomic and Another common characteristic of flavobacteria is their three domains of life. metaproteomic studies, which differ in terms of the ability to move rapidly across surfaces via gliding. The

694 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

Phytoplankton

DOM Motility adhesin Membrane- Extracellular TBDT associated enzyme system hydrolytic ATP ABC-type ATP enzyme ATP transporters synthase + H ADP

H+ Rhodopsins Secondary Na+ transporter hν h Cl– ν hν Adhesins POM Virulence factors

Figure 5 | Physiological features of flavobacteria that facilitate associations with phytoplankton. Flavobacteria Nature Reviews | Microbiology genomes encode several physiological processes that probably contribute to their interactions with phytoplankton and phytoplankton-derived organic matter. These include membrane-associated and extracellular hydrolytic enzymes, such as laminarinases and β-D-fucosidases, for the degradation of high molecular weight compounds that cannot pass through bacterial cell membranes. Flavobacteria have highly efficient, multiprotein extracellular systems that bind to large molecules, enzymatically digest them, and then shuttle the products through dedicated transport systems, such as TonB-dependent transport (TBDT) systems. Flavobacteria have additional transporters that are both ATP-dependent (ATP-binding cassette (ABC)-type) and ATP-independent (that is, secondary transporters) that facilitate the uptake of low molecular weight components of phytoplankton dissolved organic matter (DOM). Some strains have cell surface motility adhesins, such as SprB and RemA, which are necessary for gliding motility over surfaces. Other surface proteins, which are predicted to be adhesins owing to the presence of conserved, repetitive peptide motifs, may facilitate attachment to both living and dead surfaces, such as particulate organic matter (POM). Virulence factors, such as proteases, are encoded in some flavobacteria genomes and might have algicidal properties. Many flavobacteria genomes also encode rhodopsins that function as light-driven ion (H+, Cl–, or Na+) pumps. Although their function during phytoplankton blooms has not been elucidated, H+ and Na+ gradients can be used to drive substrate translocation or ATP production via ATP synthases, whereas Cl– pumps are probably involved in maintaining an appropriate intracellular ion balance.

specific mechanism of gliding is not fully understood, type A and fasciclin, are also present in many flavobacte- but it seems to be unique to Bacteroidetes and involves ria genomes110. Finally, flavobacteria seem to be adapted the production of a ‘slime layer’ of exopolysaccharides to scavenge any energy source that is produced during and mobile cell surface adhesins (known as SprB and phytoplankton growth, including hydrogen gas, which RemA in Flavobacterium johnsoniae) that are propelled is produced in the ocean during nitrogen gas fixation123. by a gliding motor121 (FIG. 5). This trait might facilitate Although the same organisms that fix nitrogen also recy- the exploration and colonization of growth substrates16 cle hydrogen, some hydrogen is released into the environ- and might also have a predatory role, as it has been sug- ment, where it could be used as a readily available energy gested that flavobacteria prey on other bacterioplankton source. Hydrogen uptake genes have been described in species122. Additional adhesins that have been implicated the SAGs of the environmental flavobacteria MS024‑2A in cell surface and cell–cell interactions, including those and MS024‑3C, which may better represent the genetic that contain peptide motifs that are conserved in all repertoire of flavobacteria than cultivated strains, as domains of life, such as cadherin, von Willebrand factor indicated by oceanic metagenomic data110.

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 695

Outlook phytoplankton organic matter124, which is an intrigu- Heterotrophic bacterial transformations determine the ing idea that warrants further investigation. Although fate of carbon that is fixed by phytoplankton, and in some flavobacterial genome sequences suggest that doing so, these ‘master recyclers’ determine the bal- flavobacteria–phytoplankton interactions may not ance of carbon remineralization and sequestration. be restricted to the transformation of senescent mat The nearly universal positive response, in terms of erial108,118,120, current evidence (albeit from studies with abundance and activity, of flavobacteria and roseobac- a relatively limited number of strains45,72) suggests that ters to phytoplankton bloom conditions is surprising roseobacter–phytoplankton interactions are more inti- given the immense variation in biological, chemical mate than those that are typically observed for flavo- and physical characteristics of blooms and the diver- bacteria. Further studies that are aimed at elucidating sity of functional activities that is encoded by these the underlying mechanisms that lead to these highly two distinct bacterial lineages. However, it is likely that specific interactions are needed. In addition, the role, the metabolic versatility of these two bacterial groups if any, of light-driven ion pumps (both bacteriochloro- facilitates their rapid response to the transient nutrient phyll a- and rhodopsin-based pumps) in the energetics pulses that are characteristic of phytoplankton blooms. of transforming phytoplankton-derived organic matter The remarkable ability of flavobacteria to transform remains an area that needs to be explored. Addressing HMW compounds of phytoplankton-derived organic all of these questions requires the continued develop- matter contrast with the seemingly limited collection ment and characterization of environmentally relevant of extracellular and cell surface-associated enzymes that phytoplankton–bacteria models. Such models are valu- are produced by roseobacters. Indeed, it has been sug- able tools for elucidating the specific nature of both inti- gested that flavobacteria and roseobacters may function mate and general interactions among the most abundant synergistically to remineralize the larger components of primary and secondary producers in the oceans.

1. Ducklow, H. W., Kirchman, D. L., Quinby, H. L., 15. Buchan, A., Gonzalez, J. M. & Moran, M. A. Overview 30. Riemann, L., Steward, G. F. & Azam, F. Dynamics of Carlson, C. A. & Dam, H. G. Stocks and dynamics of of the marine Roseobacter lineage. Appl. Environ. bacterial community composition and activity during a bacterioplankton carbon during the spring bloom in Microbiol. 71, 5665–5677 (2005). mesocosm diatom bloom. Appl. Environ. Microbiol. the eastern northern Atlantic Ocean. Deep-Sea Res. 16. Kirchman, D. L. The ecology of Cytophaga– 66, 578–587 (2000). Part II Top. Studies Oceanogr. 40, 245–263 (1993). Flavobacteria in aquatic environments. FEMS This is one of the initial papers that reports the 2. Cole, J. J., Findlay, S. & Pace, M. L. Bacterial Microbiol. Ecol. 39, 91–100 (2002). phenotypic and phylogenetic changes that occur to production in fresh and saltwater ecosystems: a cross- 17. Teeling, H. et al. Substrate-controlled succession of the bacterial community during the formation and system overview. Marine Ecol. Prog. Ser. 43, 1–10 marine bacterioplankton populations induced by a decay of a phytoplankton bloom. (1988). phytoplankton bloom. Science 336, 608–611(2012). 31. Yager, P. L. et al. Dynamic bacterial and viral response 3. Eppley, R. W. & Peterson, B. J. Particulate organic This is a comprehensive study of bacterial to an algal bloom at subzero temperatures. Limnol. matter flux and planktonic new production in the deep populations in a natural phytoplankton bloom using Oceanogr. 46, 790–801 (2001). ocean. Nature 282, 677–680 (1979). state‑of‑the-art methodologies to link bacterial 32. Taylor, M. H., Losch, M. & Bracher, A. On the drivers of 4. Behrenfeld, M. J. et al. Climate-driven trends in community structure and function. phytoplankton blooms in the Antarctic marginal ice contemporary ocean productivity. Nature 444, 18. Smetacek, V. & Cloern, J. E. Oceans. On phytoplankton zone: a modeling approach. J. Geophys. Res. Oceans 752–755 (2006). trends. Science 319, 1346–1348 (2008). 118, 63–75 (2013). 5. Behrenfeld, M. J., Boss, E., Siegel, D. A. & Shea, D. M. 19. Behrenfeld, M. J. Abandoning Sverdrup’s Critical 33. Bratbak, G., Wilson, W. & Heldal, M. Viral control of Carbon-based ocean productivity and phytoplankton Depth Hypothesis on phytoplankton blooms. Ecology Emiliania huxleyi blooms? J. Marine Systems 9, physiology from space. Global Biogeochem. Cycles 19, 91, 977–989 (2010). 75–81 (1996). GB1006 (2005). 20. Taylor, J. R. & Ferrari, R. Shutdown of turbulent 34. Smith, D. C., Simon, M., Alldredge, A. L. & Azam, F. 6. Azam, F. & Malfatti, F. Microbial structuring of marine convection as a new criterion for the onset of spring Intense hydrolytic enzyme activity on marine ecosystems. Nature 10, 782–791 (2007). phytoplankton blooms. Limnol. Oceanogr. 56, aggregates and implicates for rapid particle 7. Azam, F. et al. The ecological role of water-column 2293–2307 (2011). dissolution. Nature 359, 139–142 (1992). microbes in the sea. Marine Ecol. Prog. Ser. 10, 21. Tyrrell, T. & Merico, A. in Coccolithophores: from This paper reports that particle dissolution occurs 257–263 (1983). molecular processes to global impacts (eds rapidly owing to the extremely high levels of This is one of the first papers to introduce the Thierstein, H. R. & Young, J. R.) 75–97 (Springer, 2004). bacterial hydrolytic activity, despite the fact that concept of the microbial loop. 22. Lessard, E. J., Merico, A. & Tyrrell, T. the bacteria that produce the enzymes do not use 8. Jiao, N. et al. Microbial production of recalcitrant Nitrate:phosphate ratios and Emiliania huxleyi all of the products of hydrolysis. dissolved organic matter: long-term carbon storage in blooms. Limnol. Oceanogr. 50, 1020–1024 (2005). 35. Passow, U. Transparent exopolymer particles (TEP) in the global ocean. Nature Rev. Microbiol. 8, 593–599 23. Schoemann, V., Becquevort, S., Stefels, J., aquatic environments. Progress Oceanogr. 55, (2010). Rousseau, W. & Lancelot, C. Phaeocystis blooms in the 287–333 (2002). This review provides the first description of the global ocean and their controlling mechanisms: a 36. Moran, M. A., Reisch, C. R., Kiene, R. P. & microbial carbon pump hypothesis and its effect on review. J. Sea Res. 53, 43–66 (2005). Whitman, W. B. Genomic insights into bacterial DMSP long-term carbon sequestration in the ocean. 24. Egge, J. K. & Aksnes, D. L. Silicate as regulating transformations. Ann. Rev. Mar. Sci. 4, 523–542 (2012). 9. Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient nutrient in phytoplankton competition. Marine Ecol. This is a comprehensive review of DMSP cycles in the sea. Bioscience 49, 781–788 (1999). Prog. Ser. 83, 281–289 (1992). transformation pathways in marine bacteria. 10. Bjornsen, P. K. Phytoplankton exudation of organic 25. Martin, A. The seasonal smorgasbord of the seas. 37. Charlson, R., Lovelock, J., Andreae, M. & Warren, S. matter: why do healthy cells do it? Limnol. Oceanogr. Science 337, 46–47 (2012). Oceanic phytoplankton, atmospheric sulphur, cloud 33, 151–154 (1988). 26. Chang, F. H., Zeldis, J., Gall, M. & Hall, J. Seasonal albedo and climate. Nature 326, 655–661 (1987). 11. Biddanda, B. & Benner, R. Carbon, nitrogen, and and spatial variation of phytoplankton assemblages, This study describes the CLAW hypothesis, which carbohydrate fluxes during the production of biomass and cell size from spring to summer across proposes that phytoplankton-produced DMS has a particulate and dissolved organic matter by marine the north-eastern New Zealand continental shelf. key role in climate regulation. The CLAW acronym phytoplankton. Limnol. Oceanogr. 42, 506–518 J. Plankton Res. 25, 737–758 (2003). comes from the first letters of the surnames of the (1997). 27. Sanderson, M. P. et al. Phytoplankton and bacterial authors. 12. Fernandez, E., Serret, P., Demadariaga, I., uptake of inorganic and organic nitrogen during an 38. Orellana, M. V. et al. Marine microgels as a source of Harbour, D. S. & Davies, A. G. Photosynthetic carbon induced bloom of Phaeocystis pouchetii. Aquat. cloud condensation nuclei in the high Arctic. Proc. Natl metabolism and biochemical composition of spring Microb. Ecol. 51, 153–168 (2008). Acad. Sci. USA 108, 13612–13617 (2011). phytoplankton assemblages enclosed in microcosms: 28. Castberg, T. et al. Microbial population dynamics This study reports the role of microgels (which are the diatom–Phaeocystis sp. succession. Marine Ecol. and diversity during a bloom of the marine produced by phytoplankton) in cloud formation and Prog. Ser. 90, 89–102 (1992). coccolithophorid Emiliania huxleyi (Haptophyta). their possible effects on climate. 13. Reitan, K. I., Rainuzzo, J. R. & Olsen, Y. Effect of Marine Ecol. Prog. Ser. 221, 39–46 (2001). 39. Bird, D. F. & Karl, D. M. Uncoupling of bacteria and nutrient limitation on fatty acid and lipid content of 29. Loeder, M. G. J., Meunier, C., Wiltshire, K. H., phytoplankton during the austral spring bloom in marine microalgae J. Phycol. 30, 972–979 (1994). Boersma, M. & Aberle, N. The role of ciliates, Gerlache Strait, Antarctic Peninsula. Aquat. Microb. 14. van Rijssel, M., Janse, I., Noordkamp, D. J. B. & heterotrophic dinoflagellates and copepods in Ecol. 19, 13–27 (1999). Gieskes, W. W. C. An inventory of factors that affect structuring spring plankton communities at Helgoland 40. Arrieta, J. M. & Herndl, G. I. Changes in bacterial polysaccharide production by Phaeocystis globosa. Roads, North Sea. Marine Biol. 158, 1551–1580 β‑glucosidase diversity during a coastal phytoplankton J. Sea Res. 43, 297–306 (2000). (2011). bloom. Limnol. Oceanogr. 47, 594–599 (2002).

696 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro

41. Pernthaler, J. Predation on prokaryotes in the water and metaproteomics. Environ. Microbiol. 15, 87. Moran, M. A. et al. Ecological genomics of marine column and its ecological implications. Nature Rev. 1302–1317(2013). roseobacters. Appl. Environ. Microbiol. 73, Microbiol. 3, 637–646 (2005). 65. Holmfeldt, K., Middelboe, M., Nybroe, O. & 4559–4569 (2007). 42. Bratbak, G., Jacobsen, A. & Heldal, M. Viral lysis of Riemann, L. Large variabilities in host strain 88. González, J. M., Kiene, R. P. & Moran, M. A. Phaeocystis pouchetii and bacterial secondary susceptibility and phage host range govern Transformation of sulfur compounds by an abundant production. Aquat. Microb. Ecol. 16, 11–16 (1998). interactions between lytic marine phages and their lineage of marine bacteria in the α-subclass of the class 43. Hellebust, J. A. Excretion of some organic compounds Flavobacterium hosts. Appl. Environ. Microbiol. 73, Proteobacteria. Appl. Environ. Microbiol. 65, by marine phytoplankton. Limnol. Oceanogr. 10, 6730–6739 (2007). 3810–3819 (1999). 192–206 (1965). 66. Georges, A. A., El‑Swais, H., Craig, S. E., Li, W. K. & 89. Chen, Y. Comparative genomics of methylated amine 44. Myklestad, S. M. in The Handbook of Environmental Walsh, D. A. Metaproteomic analysis of a winter to utilization by marine Roseobacter clade bacteria and Chemistry Vol. 5D (ed. Wangersky, P.) 111–148 spring succession in coastal northwest Atlantic Ocean development of functional gene markers (tmm, gmaS). (Springer, 2000). microbial plankton. ISME J. 8, 1301–1313 (2014). Environ. Microbiol. 14, 2308–2322 (2012). 45. Miller, T. R., Hnilicka, K., Dziedzic, A., Desplats, P. & 67. Campbell, B. J. & Kirchman, D. L. Bacterial diversity, 90. Miller, M. B. & Bassler, B. L. Quorum sensing in Belas, R. Chemotaxis of Silicibacter sp. strain TM1040 community structure and potential growth rates along bacteria. Annu. Rev. Microbiol. 55, 165–199 toward dinoflagellate products. Appl. Environ. an estuarine salinity gradient. ISME J. 7, 210–220 (2001). Microbiol. 70, 4692–4701 (2004). (2013). 91. Berger, M., Neumann, R., Schulz, S., Simon, M. & 46. Bratbak, G. & Thingstad, T. F. Phytoplankton–bacteria 68. Giovannoni, S. J. & Rappe, M. in Microbial Ecology of Brinkhoff, T. Tropodithietic acid production in interactions: an apparent paradox? Analysis of a the Oceans (eds Kirchman, D. L.) 47–84 (John Wiley & Phaeobacter gallaeciensis is regulated by N‑acyl model system with both competition and Sons, 2000). homoserine lactone-mediated quorum sensing. commensalism. Marine Ecol. Prog. Ser. 25, 23–30 This book chapter provides an early review of the J. Bacteriol. 193, 6576–6585 (2011). (1985). different groups of marine bacteria on the basis of 92. Geng, H. & Belas, R. Expression of tropodithietic acid 47. Danger, M., Leflaive, J., Oumarou, C., Ten-Hage, L. & culture-independent surveys. biosynthesis is controlled by a novel autoinducer. Lacroix, G. Control of phytoplankton–bacteria 69. Goecke, F., Thiel, V., Wiese, J., Labes, A. & Imhoff, J. F. J. Bacteriol. 192, 4377–4387(2010). interactions by stoichiometric constraints. Oikos 116, Algae as an important environment for bacteria– 93. Cude, W. N. et al. Production of the antimicrobial 1079–1086 (2007). phylogenetic relationships among new bacterial species secondary metabolite indigoidine contributes to 48. Proctor, L. & Fuhrman, J. A. Roles of viral infection in isolated from algae. Phycologia 52, 14–24 (2013). competitive surface colonization by the marine organic particle flux. Marine Ecol. Prog. Ser. 69, 133– 70. Wagner-Doebler, I. et al. The complete genome roseobacter Phaeobacter sp. strain Y4I. Appl. Environ. 142 (1991). sequence of the algal symbiont Dinoroseobacter Microbiol. 78, 4771–4780 (2012). 49. Kujawinski, E. B. The impact of microbial metabolism shibae: a hitchhiker’s guide to life in the sea. ISME J. 4, 94. Wagner-Döbler, I. et al. Discovery of complex mixtures on marine dissolved organic matter. Annu. Rev. Marine 61–77 (2010). of novel long-chain quorum sensing signals in free- Sci. 3, 567–599 (2011). 71. Mayali, X., Franks, P. J. S. & Burton, R. S. Temporal living and host-associated marine alphaproteobacteria. 50. Arnosti, C. Microbial extracellular enzymes and the attachment dynamics by distinct bacterial taxa during ChemBioChem 6, 2195–2206 (2005). marine carbon cycle. Annu. Rev. Marine Sci. 3, a dinoflagellate bloom. Aquat. Microb. Ecol. 63, 95. Schaefer, A. L. et al. A new class of homoserine 401–425 (2010). 111–122 (2011). lactone quorum-sensing signals. Nature 454, 51. Stoderegger, K. E. & Herndl, G. J. Dynamics in 72. Seyedsayamdost, M. R., Case, R. J., Kolter, R. & Clardy, J. 595–599 (2008). bacterial surface properties of a natural bacterial The Jekyll-and-Hyde chemistry of Phaeobacter 96. Rao, D., Webb, J. S. & Kjelleberg, S. Microbial community in the coastal North Sea during a spring gallaciensis. Nature Chem. 3, 331–335 (2011). colonization and competition on the marine alga Ulva phytoplankton bloom. FEMS Microbiol. Ecol. 53, 73. Falkowski, P. G. et al. The evolution of modern eukaryotic australis. Appl. Environ. Microbiol. 72, 5547–5555 285–294 (2005). phytoplankton. Science 305, 354–360 (2004). (2006). 52. Grossart, H. P. & Ploug, H. Microbial degradation of 74. Luo, H., Csűros, M., Hughes, A. L. & Moran, M. A. 97. González, J. M., Mayer, F., Moran, M. A., organic carbon and nitrogen on diatom aggregates. Evolution of divergent life history strategies in marine Hodson, R. E. & Whitman, W. B. Sagittula stellata gen. Limnol. Oceanogr. 46, 267–277 (2001). Alphaproteobacteria. mBio 4, e00373-13 (2013). nov, sp. nov, a lignin-transforming bacterium from a 53. Hopkinson, C. S. & Vallino, J. J. Efficient export of 75. Amin, S. A., Parker, M. S. & Armbrust, E. V. coastal environment. Int. J. Systemat. Bacteriol. 47, carbon to the deep ocean through dissolved organic Interactions between diatoms and bacteria. Microbiol. 773–780 (1997). matter. Nature 433, 142–145 (2005). Mol. Biol. Rev. 76, 667–684 (2012). 98. Alavi, M., Miller, T., Erlandson, K., Schneider, R. & 54. Ogawa, H., Amagai, Y., Koike, I., Kaiser, K. & 76. Wagner-Döbler, I. & Bibel, H. Environmental biology of Belas, R. Bacterial community associated with Benner, R. Production of refractory dissolved organic the marine Roseobacter lineage. Annu. Rev. Microbiol. Pfiesteria-like dinoflagellate cultures. Environ. matter by bacteria. Science 292, 917–920 (2001). 60, 255–280 (2006). Microbiol. 3, 380–396 (2001). 55. Pinhassi, J. et al. Changes in bacterioplankton 77. Newton, R. J. et al. Genome characteristics of a 99. Archer, S. D., Tarran, G. A., Stephens, J. A., composition under different phytoplankton regimens. generalist marine bacterial lineage. ISME J. 4, Butcher, L. J. & Kimmance, S. A. Combining flow Appl. Environ. Microbiol. 70, 6753–6766 (2004). 784–798 (2010). sorting with gas chromatography to determine 56. Zubkov, M. V. et al. Linking the composition of 78. Giovannoni, S. J. et al. Genome streamlining in a phytoplankton group-specific intracellular content of bacterioplankton to rapid turnover of dissolved cosmopolitan oceanic bacterium. Science 309, dimethylsulphioniopropionate (DMSP). Aquat. Microb. dimethylsulphoniopropionate in an algal bloom in the 1242–1245 (2005). Ecol. 62, 109–121 (2011). North Sea. Environ. Microbiol. 3, 304–311 (2001). 79. Rocap, G. et al. Genomic divergence in two 100. Stefels, J., Steinke, M., Turner, S., Malin, G. & 57. Stepanauskas, R., Moran, M. A., Bergamaschi, B. A. & Prochlorococcus ecotypes reflects oceanic niche Belviso, S. Environmental constraints on the Hollibaugh, J. T. Covariance of bacterioplankton differentiation. Nature 424, 1042–1047 (2003). production and removal of the climatically active gas composition and environmental variables in a 80. Ottesen, E. A. et al. Metatranscriptomic analysis of dimethylsulphide (DMS) and implications for temperate delta system. Aquat. Microb. Ecol. 31, autonomously collected and preserved marine ecosystem modelling. Biogeochemistry 83, 245–275 85–98 (2003). bacterioplankton. ISME J. 5, 1881–1895 (2011). (2007). 58. Alonso-Saez, L. & Gasol, J. M. Seasonal variations in 81. Luo, H., Loytynoja, A. & Moran, M. A. Genome 101. Kiene, R. P., Linn, L. J. & Bruton, J. A. New and the contributions of different bacterial groups to the content of uncultivated marine roseobacters in the important roles for DMSP in marine microbial uptake of low-molecular-weight compounds in surface ocean. Environ. Microbiol. 14, 41–51 (2011). communities. J. Sea Res. 43, 209–224 (2000). northwestern Mediterranean coastal waters. Appl. 82. Shiba, T. Roseobacter litoralis gen. nov., sp. nov., and 102. Todd, J. D., Kirkwood, M., Newton-Payne, S. & Environ. Microbiol. 73, 3528–3535 (2007). Roseobacter denitrificans sp. nov., aerobic pink- Johnston, A. W. B. DddW, a third DMSP lyase in a 59. Pinhassi, J. & Berman, T. Differential growth response pigmented bacteria which contain model roseobacter marine bacterium, Ruegeria of colony-forming α- and γ-proteobacteria in dilution bacteriochlorophyll a. System. Appl. Microbiol. 14, pomeroyi DSS‑3. ISME J. 6, 223–226 (2012). culture and nutrient addition experiments from Lake 140–145 (1991). 103. Cottrell, M. T. & Kirchman, D. L. Community Kinneret (Israel), the eastern Mediterranean Sea, and This article formally describes the first species of composition of marine bacterioplankton determined the Gulf of Eilat. Appl. Environ. Microbiol. 69, bacteria in the Roseobacter clade, with an by 16S rRNA gene clone libraries and fluorescence 199–211 (2003). emphasis on their ability to synthesize pigments to in situ hybridization. Appl. Environ. Microbiol. 66, 60. Grossart, H. P., Levold, F., Allgaier, M., Simon, M. & make use of light. 5116–5122 (2000). Brinkhoff, T. Marine diatom species harbour distinct 83. Mayali, X., Franks, P. J. S. & Azam, F. Cultivation and 104. Alonso, C., Warnecke, F., Amann, R. & Pernthaler, J. bacterial communities. Environ. Microbiol. 7, ecosystem role of a marine Roseobacter clade- High local and global diversity of Flavobacteria in 860–873 (2005). affiliated cluster bacterium. Appl. Environ. Microbiol. marine plankton. Environ. Microbiol. 9, 1253–1266 61. LeCleir, G. R., DeBruyn, J. M., Maas, E. W., Boyd, P. W. 74, 2595–2603 (2008). (2007). & Wilhelm, S. W. Temporal changes in particle- 84. Alavi, M. R. Predator/prey interaction between 105. Simon, M., Glockner, F. O. & Amann, R. Different associated microbial communities after interception by Pfiesteria piscicida and Rhodomonas mediated by a community structure and temperature optima of nonlethal sediment traps. FEMS Microbiol. Ecol. 87, marine α-proteobacterium. Microb. Ecol. 47, 48–58 heterotrophic picoplankton in various regions of the 153–163 (2014). (2004). Southern Ocean. Aquat. Microb. Ecol. 18, 275–284 62. Fandino, L. B., Riemann, L., Steward, G. F., Long, R. A. 85. Sharifah, E. N. & Eguchi, M. The phytoplankton (1999). & Azam, F. Variations in bacterial community structure Nannochloropsis oculata enhances the ability of 106. Bauer, M. et al. Whole genome analysis of the marine during a dinoflagellate bloom analyzed by DGGE and Roseobacter clade bacteria to inhibit the growth of fish Bacteroidetes ‘Gramella forsetii’ reveals adaptations to 16S rDNA sequencing. Aquat. Microb. Ecol. 23, pathogen Vibrio anguillarum. PLoS ONE 6, e26756 degradation of polymeric organic matter. Environ. 119–130 (2001). (2011). Microbiol. 8, 2201–2213 (2006). 63. Rink, B. et al. Effects of phytoplankton bloom in a 86. Amaro, A. M., Fuentes, M. S., Ogalde, S. R., 107. Gómez-Consarnau, L. et al. Light stimulates growth of coastal ecosystem on the composition of bacterial Venegas, J. A. & Suarez-Isla, B. A. Identification and proteorhodopsin-containing marine Flavobacteria. communities. Aquat. Microb. Ecol. 48, 47–60 (2007). characterization of potentially algal-lytic marine Nature 445, 210–213 (2007). 64. Williams, T. J. et al. The role of planktonic bacteria strongly associated with the toxic This article describes the growth of flavobacteria in Flavobacteria in processing algal organic matter in dinoflagellate Alexandrium catenella. J. Eukaryot. response to light owing to expression of the coastal East Antarctica revealed using metagenomics Microbiol. 52, 191–200 (2005). proteorhodopsin gene.

NATURE REVIEWS | MICROBIOLOGY VOLUME 12 | OCTOBER 2014 | 697

108. González, J. M. et al. Genomics of the 122. Banning, E. C., Casciotti, K. L. & Kujawinski, E. B. 137. Shutler, J. D. et al. Coccolithophore surface proteorhodopsin-containing marine flavobacterium Novel strains isolated from a coastal aquifer suggest a distributions in the North Atlantic and their

Dokdonia sp. strain MED134. Appl. Environ. predatory role for flavobacteria. FEMS Microbiol. Ecol. modulation of the air–sea flux of CO2 from 10 years of Microbiol. 77, 8676–8686 (2011). 73, 254–270 (2010). satellite Earth observation data. Biogeosciences 10, 109. Qin, Q. L. et al. The complete genome of 123. Lambert, G. R. & Smith, G. D. The hydrogen 2699–2709 (2013). Zunongwangia profunda SM‑A87 reveals its metabolism of cyanobacteria (blue-green algae). Biol. 138. Merico, A., Tyrrell, T. & Cokacar, T. Is there any adaptation to the deep-sea environment and ecological Rev. 56, 589–660 (1981). relationship between phytoplankton seasonal role in sedimentary organic nitrogen degradation. 124. Taylor, J. D., Cottingham, S. D., Billinge, J. & dynamics and the carbonate system? J. Marine BMC Genomics 11, 247 (2010). Cunliffe, M. Seasonal microbial community dynamics Systems 59, 120–142 (2006). 110. Woyke, T. et al. Assembling the marine metagenome, correlate with phytoplankton-derived polysaccharides 139. Iglesias-Rodríguez, M. D. et al. Representing key one cell at a time. PLoS ONE 4, e5299 (2009). in surface coastal waters. ISME J. 8, 245–248 (2014). phytoplankton functional groups in ocean carbon cycle 111. Gómez-Pereira, P. R. et al. Genomic content of 125. Buchan, A., Hadden, M. & Suzuki, M. T. Development models: coccolithophorids. Global Biogeochem. Cycles uncultured Bacteroidetes from contrasting oceanic and application of quantiative PCR tools for subgroups 16, 1100 (2002). provinces in the North Atlantic Ocean. Environ. of the Roseobacter clade. Appl. Environ. Microbiol. 140. Harada, N. et al. Enhancement of coccolithophorid Microbiol. 14, 52–66 (2012). 75, 7543–7547 (2009). blooms in the Bering Sea by recent environmental 112. Fernandez-Gomez, B. et al. Ecology of marine 126. Jooste, P. J. & Hugo, C. J. The taxonomy, ecology and changes. Global Biogeochem. Cycles 26, GB2036 Bacteroidetes: a comparative genomics approach. cultivation of bacterial genera belonging to the family (2012). ISME J. 7, 1026–1037 (2013). Flavobacteriaceae. Int. J. Food Microbiol. 53, 81–94 141. Wilson, W. H. et al. Isolation of viruses responsible for 113. Thomas, F., Hehemann, J.‑H., Rebuffet, E., Czjzek, M. (1999). the demise of an Emiliania huxleyi bloom in the & Michel, G. Environmental and gut bacteroidetes: the 127. Ludwig, W., Euzeby, J. P. & Whitman, W. B. in Bergey’s English Channel. J. Marine Biol. Associ. 82, 369–377 food connection. Frontiers Microbiol. 2, 93–93 (2011). Manual of Systematic Bacteriology Vol. 4 (eds Krieg, (2002). 114. Rinta-Kanto, J. M., Sun, S., Sharma, S., Kiene, R. P. & N. R. et al.) (Bergey’s Manual Trust, 2010). 142. Peperzak, L. & Gaebler-Schwarz, S. Current knowledge Moran, M. A. Bacterial community transcription 128. Hayes, P. R. Studies on marine Flavobacteria. of the life cycles of Phaeocystis globosa and patterns during a marine phytoplankton bloom. J. General Microbiol. 30, 1–19 (1963). Phaeocystis antarctica (Prymnesiophyceae) J. Phycol. Environ. Microbiol. 14, 228–239 (2012). 129. Cushing, D. H. A difference in structure between 48, 514–517 (2012). 115. Reeves, A. R., Wang, G.‑R. & Salyers, A. A. ecosystems in strongly stratified waters and in those 143. Alderkamp, A. C. et al. Dynamics in carbohydrate Characterization of four outer membrane proteins that that are only weakly stratified. J. Plankton Res. 11, composition of Phaeocystis pouchetii colonies during play a role in utilization of starch by Bacteroides 1–13 (1989). spring blooms in mesocosms. J. Sea Res. 55, 169–181 thetaiotaomicron. J. Bacteriol. 179, 643–649 (1997). 130. Kooistra, W. H. C. F., Gersonde, R., Medlin, L. K. & (2006). 116. González, J. et al. Genome analysis of the Mann, D. G. in Evolution of Primary Producers in the 144. Brussaard, C. P. D., Gast, G. J., van Duyl, F. C. & proteorhodopsin-containing marine bacterium Sea (eds Falkowski, P. G. & Knoll, A. H.) (Academic Riegman, R. Impact of phytoplankton bloom Polaribacter sp. MED152 (Flavobacteria). Proc. Natl Press, 2007). magnitude on a pelagic microbial food web. Marine Acad. Sci. USA 105, 8724–8729 (2008). 131. Falkowski, P. G., Barber, R. T. & Smetacek, V. Ecol. Progress Series 144, 211–221 (1996). 117. Yoshizawa, S. et al. Functional characterization of Biogeochemical controls and feedbacks on ocean 145. Nejstgaard, J. C. et al. Zooplankton grazing on flavobacteria rhodopsins reveals a unique class of light- primary production. Science 281, 200–206 (1998). Phaeocystis: a quantitative review and future driven chloride pump in bacteria. Proc. Natl Acad. Sci. 132. Nelson, D. M., Treguer, P., Brzezinski, M. A., challenges. Biogeochemistry 83, 147–172 USA 111, 6732–6737 (2014). Leynaert, A. & Queguiner, B. Production and (2007). This paper describes the first example of a dissolution of biogenic silica in the ocean: revised 146. Rousseau, V. et al. Characterization of Phaeocystis rhodopsin chloride pump found in flavobacteria. global estimates, comparision with regional data and globosa (Prymnesiophyceae), the blooming species in 118. Sohn, J. H. et al. Kordia algicida gen. nov., sp nov., an relationship to biogenic sedimentation. Global the Southern North Sea. J. Sea Res. 76, 105–113 algicidal bacterium isolated from red tide. Int. Biogeochem. Cycles 9, 359–372 (1995). (2013). J. Systemat. Evol. Microbiol. 54, 675–680 (2004). 133. Kroger, N. & Poulsen, N. Diatoms — from cell wall 119. Skerratt, J. H., Bowman, J. P., Hallegraeff, G., biogenesis to nanotechnology. Annu. Rev. Genet. 42, James, S. & Nichols, P. D. Algicidal bacteria associated 83–107 (2008). Acknowledgements with blooms of a toxic dinoflagellate in a temperate 134. Sumper, M. & Brunner, E. Silica biomineralisation in A.B. acknowledges support from the US National Science Australian estuary. Marine Ecol. Prog. Ser. 244, 1–15 diatoms: the model organism Thalassiosira Foundation Division of Ocean Sciences (OCE-0550485 and (2002). pseudonana. ChemBioChem 9, 1187–1194 (2008). OCE-1061352). J.M.G. was supported by the CONSOLIDER- 120. Goecke, F., Labes, A., Wiese, J. & Imhoff, J. F. Chemical 135. Henderiks, J. & Rickaby, R. E. M. A coccolithophore INGENIO2010 Program (CSD2008-00077) and MarineGems interactions between marine macroalgae and bacteria. concept for constraining the Cenozoic carbon cycle. (CTM2010-20361) from the Spanish Ministry of Science and Marine Ecol. Prog. Ser. 409, 267–299 (2010). Biogeosciences 4, 323–329 (2007). Innovation. 121. McBride, M. J. Bacterial gliding motility: multiple 136. Legendre, L. & Lefevre, J. Microbial food webs and the mechanisms for cell movement over surfaces. Annu. export of biogenic carbon in oceans. Aquat. Microb. Competing interests statement Rev. Microbiol. 55, 49–75 (2001). Ecol. 9, 69–77 (1995). The authors declare no competing interests.

698 | OCTOBER 2014 | VOLUME 12 www.nature.com/reviews/micro